Fitopatologia - Artigos

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Revisiting the classification of curtoviruses based on genome-wide pairwise identity
(Archives of Virology, 2014-01-25) Zerbini, F. Murilo; Varsani, Arvind; Martin, Darren P.; Navas-Castillo, Jesús; Moriones, Enrique; Hernández-Zepeda, Cecilia; Idris, Ali; Brown, Judith K.
Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77 % genome-wide pairwise identity as a species demarcation threshold and 94 % genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77 % genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94 % identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV).
Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus
(Archives of Virology, 2014-03-22) Zerbini, F. Murilo; Varsani, Arvind; Navas-Castillo, Jesús; Moriones, Enrique; Hernández-Zepeda, Cecilia; Idris, Ali; Brown, Judith K.; Martin, Darren P.
The family Geminiviridae includes plant-infecting circular single-stranded DNA viruses that have geminate particle morphology. Members of this family infect both monocotyledonous and dicotyledonous plants and have a nearly global distribution. With the advent of new molecular tools and low-cost sequencing, there has been a significant increase in the discovery of new geminiviruses in various cultivated and non-cultivated plants. In this communication, we highlight the establishment of three new genera (Becurtovirus, Eragrovirus and Turncurtovirus) to accommodate various recently discovered geminiviruses that are highly divergent and, in some cases, have unique genome architectures. The genus Becurtovirus has two viral species, Beet curly top Iran virus (28 isolates; leafhopper vector Circulifer haematoceps) and Spinach curly top Arizona virus (1 isolate; unknown vector), whereas the genera Eragrovirus and Turncurtovirus each have a single assigned species: Eragrostis curvula streak virus (6 isolates; unknown vector) and Turnip curly top virus (20 isolates; leafhopper vector Circulifer haematoceps), respectively. Based on analysis of all of the genome sequences available in public databases for each of the three new genera, we provide guidelines and protocols for species and strain classification within these three new genera.
A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae)
(Archives of Virology, 2013-01-23) Zerbini, F. Murilo; Muhire, Brejnev; Martin, Darren P.; Brown, Judith K.; Navas-Castillo, Jesús; Moriones, Enrique; Rivera-Bustamante, Rafael; Malathi, V. G.; Briddon, Rob W.; Varsani, Arvind
Recent advances in the ease with which the genomes of small circular single-stranded DNA viruses can be amplified, cloned, and sequenced have greatly accelerated the rate at which full genome sequences of mastreviruses (family Geminiviridae, genus Mastrevirus) are being deposited in public sequence databases. Although guidelines currently exist for species-level classification of newly determined, complete mastrevirus genome sequences, these are difficult to apply to large sequence datasets and are permissive enough that, effectively, a high degree of leeway exists for the proposal of new species and strains. The lack of a standardised and rigorous method for testing whether a new genome sequence deserves such a classification is resulting in increasing numbers of questionable mastrevirus species proposals. Importantly, the recommended sequence alignment and pairwise identity calculation protocols of the current guidelines could easily be modified to make the classification of newly determined mastrevirus genome sequences significantly more objective. Here, we propose modified versions of these protocols that should substantially minimise the degree of classification inconsistency that is permissible under the current system. To facilitate the objective application of these guidelines for mastrevirus species demarcation, we additionally present a user-friendly computer program, SDT (species demarcation tool), for calculating and graphically displaying pairwise genome identity scores. We apply SDT to the 939 full genome sequences of mastreviruses that were publically available in May 2012, and based on the distribution of pairwise identity scores yielded by our protocol, we propose mastrevirus species and strain demarcation thresholds of >78 % and >94 % identity, respectively.
Complete nucleotide sequences of two new begomoviruses infecting the wild malvaceous plant Melochia sp. in Brazil
(Archives of Virology, 2015-10-01) Fiallo-Olivé, Elvira; Zerbini, F. Murilo; Navas-Castillo, Jesús
Wild malvaceous plants are hosts for a large number of begomoviruses (genus Begomovirus, family Geminiviridae) in both the Old World and the New World. Here, we report the complete genome sequences of two new begomoviruses from Melochia sp. plants from Brazil. The cloned bipartite genomes, composed of DNA-A and DNA-B, showed the typical organization of the New World begomoviruses but they were distantly related to the genomes of other begomoviruses. We propose the names Melochia mosaic virus and Melochia yellow mosaic virus for these begomoviruses.

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